Atomistry » Calcium » PDB 6yd4-6ywn » 6ymr
Atomistry »
  Calcium »
    PDB 6yd4-6ywn »
      6ymr »

Calcium in PDB 6ymr: Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin

Enzymatic activity of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin

All present enzymatic activity of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin:
3.4.24.27;

Protein crystallography data

The structure of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin, PDB code: 6ymr was solved by M.Kljajic, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.67 / 1.60
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.768, 92.768, 129.602, 90, 90, 120
R / Rfree (%) 13.5 / 17.8

Other elements in 6ymr:

The structure of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin (pdb code 6ymr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin, PDB code: 6ymr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6ymr

Go back to Calcium Binding Sites List in 6ymr
Calcium binding site 1 out of 4 in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:14.3
occ:1.00
 O E:GLN61 2.3 13.3 1.0
O E:HOH582 2.3 17.0 1.0
O E:HOH709 2.4 16.4 1.0
OD1 E:ASP57 2.4 14.5 1.0
OD1 E:ASP59 2.4 14.7 1.0
O E:HOH572 2.4 15.4 1.0
OD2 E:ASP57 2.6 14.0 1.0
CG E:ASP57 2.8 13.7 1.0
H E:GLN61 3.3 14.8 1.0
CG E:ASP59 3.4 15.5 1.0
C E:GLN61 3.5 13.1 1.0
H E:ASP59 3.5 16.4 1.0
HB2 E:GLN61 3.7 19.9 1.0
OD2 E:ASP59 3.8 18.2 1.0
O E:HOH623 4.0 18.7 1.0
N E:GLN61 4.0 12.4 1.0
HA E:PHE62 4.0 15.2 1.0
CA E:GLN61 4.2 13.5 1.0
H E:ALA58 4.3 16.1 1.0
CB E:ASP57 4.3 13.6 1.0
N E:ASP59 4.3 13.7 1.0
H E:ASN60 4.4 15.4 1.0
CB E:GLN61 4.4 16.6 1.0
O E:HOH671 4.4 15.1 1.0
N E:PHE62 4.5 13.4 1.0
CB E:ASP59 4.6 13.6 1.0
OD2 E:ASP67 4.6 13.4 1.0
O E:HOH543 4.6 13.8 1.0
O E:HOH752 4.7 35.0 1.0
N E:ASN60 4.7 12.8 1.0
HB2 E:ASP57 4.7 16.3 1.0
N E:ALA58 4.7 13.5 1.0
CA E:PHE62 4.7 12.7 1.0
HB3 E:ASP57 4.8 16.3 1.0
H E:PHE63 4.8 16.6 1.0
CA E:ASP59 4.8 12.5 1.0
HA E:ASP57 4.8 16.1 1.0
HB3 E:ALA58 4.9 19.3 1.0
HB3 E:GLN61 4.9 19.9 1.0
C E:ASP59 4.9 13.5 1.0

Calcium binding site 2 out of 4 in 6ymr

Go back to Calcium Binding Sites List in 6ymr
Calcium binding site 2 out of 4 in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:14.9
occ:1.00
 O E:GLU187 2.4 15.2 1.0
OD2 E:ASP138 2.4 13.3 1.0
O E:HOH540 2.4 14.8 1.0
OD1 E:ASP185 2.4 15.6 1.0
OE1 E:GLU177 2.5 14.3 1.0
OE2 E:GLU190 2.5 15.9 1.0
OE1 E:GLU190 2.5 14.4 1.0
OE2 E:GLU177 2.8 14.9 1.0
CD E:GLU190 2.8 16.1 1.0
CD E:GLU177 2.9 13.9 1.0
CG E:ASP138 3.4 14.3 1.0
C E:GLU187 3.4 15.4 1.0
CG E:ASP185 3.5 16.8 1.0
HB3 E:ASP138 3.6 16.1 1.0
HA E:ILE188 3.6 18.2 1.0
H E:GLU187 3.7 20.9 1.0
CA E:CA404 3.8 16.3 1.0
H E:GLY189 3.8 17.4 1.0
OD2 E:ASP185 3.8 18.4 1.0
HB2 E:GLU187 3.9 24.8 1.0
CB E:ASP138 4.0 13.4 1.0
O E:ASP185 4.1 16.5 1.0
H E:GLU190 4.2 17.4 1.0
H E:ASP185 4.2 20.9 1.0
N E:GLU187 4.2 17.4 1.0
N E:ILE188 4.2 14.6 1.0
HB2 E:ASP138 4.3 16.1 1.0
OD1 E:ASP138 4.3 15.0 1.0
CA E:GLU187 4.3 17.6 1.0
CA E:ILE188 4.3 15.2 1.0
CG E:GLU190 4.3 16.4 1.0
HD13 E:ILE188 4.3 20.9 1.0
CG E:GLU177 4.4 14.9 1.0
N E:GLY189 4.5 14.5 1.0
O E:HOH539 4.5 19.4 1.0
C E:ASP185 4.6 16.6 1.0
CB E:GLU187 4.6 20.7 1.0
HG3 E:GLU190 4.6 19.6 1.0
HB2 E:GLU177 4.7 18.5 1.0
HB3 E:GLU177 4.7 18.5 1.0
CB E:ASP185 4.7 17.1 1.0
N E:ASP185 4.8 17.5 1.0
HG2 E:GLU190 4.8 19.6 1.0
C E:ILE188 4.8 14.7 1.0
HG2 E:GLU177 4.8 17.9 1.0
HA E:THR174 4.9 17.3 1.0
O E:HOH524 4.9 18.5 1.0
CB E:GLU177 4.9 15.5 1.0
HG3 E:GLU177 4.9 17.9 1.0
HB3 E:GLU190 5.0 19.8 1.0
CA E:ASP185 5.0 16.8 1.0
N E:GLU190 5.0 14.5 1.0

Calcium binding site 3 out of 4 in 6ymr

Go back to Calcium Binding Sites List in 6ymr
Calcium binding site 3 out of 4 in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:16.3
occ:1.00
 O E:ASN183 2.3 18.6 1.0
OE2 E:GLU190 2.3 15.9 1.0
O E:HOH524 2.4 18.5 1.0
OD2 E:ASP185 2.4 18.4 1.0
OE2 E:GLU177 2.4 14.9 1.0
O E:HOH546 2.4 19.7 1.0
CG E:ASP185 3.2 16.8 1.0
CD E:GLU177 3.2 13.9 1.0
CD E:GLU190 3.3 16.1 1.0
C E:ASN183 3.5 19.7 1.0
HG3 E:GLU190 3.6 19.6 1.0
HA E:PRO184 3.6 23.2 1.0
OD1 E:ASP185 3.6 15.6 1.0
HB2 E:ASN183 3.7 30.3 1.0
OE1 E:GLU177 3.8 14.3 1.0
HG2 E:GLU190 3.8 19.6 1.0
CA E:CA403 3.8 14.9 1.0
CG E:GLU190 3.8 16.4 1.0
HB3 E:ASN183 3.8 30.3 1.0
H E:ASP185 4.1 20.9 1.0
OD2 E:ASP191 4.1 20.2 1.0
CA E:PRO184 4.1 19.4 1.0
CB E:ASN183 4.2 25.3 1.0
N E:ASP185 4.2 17.5 1.0
HG2 E:GLU177 4.2 17.9 1.0
CG E:GLU177 4.2 14.9 1.0
C E:PRO184 4.3 19.7 1.0
N E:PRO184 4.3 19.8 1.0
OD1 E:ASP191 4.3 19.7 1.0
OE1 E:GLU190 4.3 14.4 1.0
HG3 E:GLU177 4.3 17.9 1.0
HB3 E:ASP185 4.3 20.5 1.0
CB E:ASP185 4.4 17.1 1.0
O E:LYS182 4.4 23.8 1.0
O E:HOH745 4.4 48.9 1.0
CA E:ASN183 4.5 23.3 1.0
O E:HOH721 4.5 50.4 1.0
CG E:ASP191 4.6 19.2 1.0
O E:PRO184 4.9 20.7 1.0
CA E:ASP185 4.9 16.8 1.0

Calcium binding site 4 out of 4 in 6ymr

Go back to Calcium Binding Sites List in 6ymr
Calcium binding site 4 out of 4 in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:19.2
occ:1.00
 O E:ILE197 2.3 26.7 1.0
OG1 E:THR194 2.3 19.7 1.0
O E:TYR193 2.3 19.1 1.0
O E:HOH683 2.4 28.3 1.0
OD1 E:ASP200 2.4 22.0 1.0
O E:HOH576 2.4 18.8 1.0
O E:THR194 2.4 20.5 1.0
C E:THR194 3.2 19.4 1.0
C E:TYR193 3.3 18.4 1.0
CB E:THR194 3.4 19.6 1.0
HB E:ILE197 3.4 34.6 1.0
CG E:ASP200 3.5 22.3 1.0
C E:ILE197 3.5 28.0 1.0
H E:ILE197 3.6 35.4 1.0
CA E:THR194 3.6 18.7 1.0
HB E:THR194 3.6 23.5 1.0
OD2 E:ASP200 3.8 22.7 1.0
N E:THR194 3.8 18.4 1.0
H E:ASP200 3.9 27.4 1.0
HA E:SER198 4.1 38.5 1.0
HB3 E:TYR193 4.1 21.6 1.0
CA E:ILE197 4.2 28.1 1.0
HD2 E:TYR193 4.2 25.6 1.0
CB E:ILE197 4.2 28.9 1.0
N E:ILE197 4.2 29.5 1.0
N E:PRO195 4.3 20.9 1.0
HA E:PRO195 4.4 28.2 1.0
O E:HOH713 4.4 50.6 1.0
HG22 E:ILE197 4.4 33.8 1.0
O E:ASP200 4.5 19.7 1.0
O E:HOH717 4.5 37.0 1.0
N E:SER198 4.5 30.9 1.0
CA E:TYR193 4.5 16.8 1.0
HA E:THR194 4.6 22.4 1.0
CG2 E:THR194 4.6 21.1 1.0
N E:ASP200 4.7 22.9 1.0
CA E:SER198 4.7 32.2 1.0
O E:GLU190 4.7 16.4 1.0
H E:THR194 4.7 22.1 1.0
CB E:TYR193 4.7 18.1 1.0
CD2 E:TYR193 4.7 21.3 1.0
CA E:PRO195 4.7 23.6 1.0
CB E:ASP200 4.8 21.9 1.0
C E:ASP200 4.8 18.8 1.0
HG23 E:THR194 4.8 25.2 1.0
H E:GLY199 4.8 33.1 1.0
HG21 E:THR194 4.9 25.2 1.0
CG2 E:ILE197 4.9 28.2 1.0
C E:SER198 4.9 30.9 1.0
CA E:ASP200 5.0 20.8 1.0

Reference:

M.Kljajic, H.-D.Gerber, A.Heine, G.Klebe. Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin To Be Published.
Page generated: Thu Jul 18 22:25:51 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy